| Tools | Category homology (H), signature (I), machine learning (II) |
Organism animal (A), plant (P) |
ML Method ML (machine learning) method: support vector machine (SVM), random forest (RF), hierarchical hidden Markov model (HHMM), best-first trees (BF-trees), Self-organizing maps (SOMs) |
Publication Span | Current Version | Aviailability | Reference |
|---|---|---|---|---|---|---|---|
| SUmirFind/SUmirFold | H | P | – | 2012 | – |  |
|
| MIReNA | H & I | A, P | – | 2010 | – | |
|
| miRDeep-P | I | P | – | 2011 | v1.3 | |
|
| miRDeep-P2 | I | P | – | 2019 | v1.1.4 | |
|
| miRNAFold | I | A, P | – | 2012–2016 | – | |
|
| miRPlant | I | P | – | 2013 | v0.1 | |
|
| miR-PREFeR | I | P | – | 2014 | |
|
|
| mirinho | I | A, P | – | 2015 | –2015 | |
|
| miRA | I | P | – | 2015 | v1.2.0 | |
|
| miRNA Digger | I | A, P | – | 2016 | –2016 | |
|
| miRvial | I | A, P | – | 2017 | v0.0.4 | |
|
| miRCat2 | I | A, P | – | 2017 | v4.5 | |
|
| triplet–SVM | II | A, P | SVM | 2005 | –2005 | |
|
| MiPred | II | A, P | RF | 2007 | v0.1 | |
|
| miRanalyzer | I & II | A, P | RF | 2009 | v0.3 | |
|
| HHMMiR | II | A, P | HHMM | 2009 | v1.2 | |
|
| miReader | I & II | A, P | BF-trees | 2013 | –2016 | |
|
| miRPlex | I & II | A, P | SVM | 2013 | v0.1 | |
|
| miRLocator | II | P | RF | 2015 | –2017 | |
|
| plantMirP | II | P | SVM | 2016 | v1.0.0 | |
|
| deepSOM | II | A, P | SOMs | 2017 | v0.19 | |
|
| Mirnovo | I & II | A, P | RF | 2017 | v1.0 | |
|
| miRHunter | II | A, P | SVM | 2017 | – | |
|
| miRNA-dis | II | A, P | SVM | 2017 | – | |
|
| microRPM | I & II | P | SVM | 2017 | –2018 | |
|